The rationale of this project is to develop a method to monitor the expression levels of a large number of genes in various experimental conditions and to understand global changes of gene expression patterns in development and aging. The systematic analysis of expression patterns of a large number of genes is rapidly becoming the method of choice for many laboratories to understand biological systems. Accordingly, the demand for high quality cDNA libraries and cDNA microarrays is increasing. The goals of this research project are to collect mouse cDNA clones and prepare cDNA microarrays containing as many mouse genes as possible. Previously we assembled and released two non-overlapping mouse gene sets: NIA Mouse 15K cDNA Clone Set, containing ~12,000 unique cDNA clones, and NIA Mouse 7.4K cDNA Clone Set, containing ~7400 unique cDNA clones. These clone sets have been freely distributed to the research community. During this period, we have continued to generate cDNA libraries and obtain cDNA sequences. We have analyzed all the ESTs that we have generated so far (a total of 249,200 high-quality EST sequences) and clustered them with public sequences to produce an index of approximately 30,000 total mouse genes that includes 977 previously unidentified genes. Analysis of gene expression levels by EST frequency identifies genes that characterize preimplantation embryos, embryonic stem cells, and adult stem cells, thus providing potential markers as well as clues to the functional features of these cells. Principal component analysis identified a set of 88 genes whose average expression levels decrease from oocytes to blastocysts, stem cells, post-implantation embryos, and finally to newborn tissues. This can be a first step towards a possible definition of a molecular scale of cellular potency. In our previous work, we developed a glass-slide microarray platform containing in situ-synthesized 60-mer oligonucleotide probes representing approximately 22,000 unique mouse transcripts, assembled primarily from sequences of stem cell and embryo cDNA libraries. We are currently working towards more comprehensive DNA microarrays containing 44,000 unique mouse transcripts/genes. The sequences and cDNA clones recovered in this work provide a comprehensive resource for genes functioning in early mouse embryos and stem cells. The nonrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine.